Discrete breathers in protein structures

@article{Piazza2008DiscreteBI,
  title={Discrete breathers in protein structures},
  author={Francesco Piazza and Yves‐Henri Sanejouand},
  journal={Physical Biology},
  year={2008},
  volume={5},
  pages={026001}
}
Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DBs) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an analytical approach, we extend our previous results to low-energy discrete breathers as well as to smaller proteins. We confirm and further scrutinize the striking site selectiveness of energy localization in the presence of spatial disorder. In particular, we find… 

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References

SHOWING 1-10 OF 90 REFERENCES
Discrete Breathers
VARIATIONAL PROOF FOR HARD DISCRETE BREATHERS IN SOME CLASSES OF HAMILTONIAN DYNAMICAL SYSTEMS
We present a new method for proving the existence of Discrete Breathers in translationally invariant Hamiltonian systems describing massive particles interacting by a short range covex potential
Discrete breathers in nonlinear network models of proteins.
TLDR
It is shown that spontaneous localization of energy occurs generically and is a site-dependent process, suggesting that nonlinear phenomena may play an important role in enzyme function, allowing for energy storage during the catalytic process.
Discrete breathers in a polyethylene chain
The existence of discrete breathers or intrinsic localized modes (localized periodic oscillations of transzigzag) is shown. In the localization region periodic contraction-extension of valence
Dimension dependent energy thresholds for discrete breathers
Discrete breathers are time-periodic, spatially localized solutions of the equations of motion for a system of classical degrees of freedom interacting on a lattice. We study the existence of energy
...
...